Read10X_output: Produce counts matrix from CellRanger output

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Produce counts matrix from CellRanger output

Description

Concatenates the three output files of CellRanger alignment.

Usage

Read10X_output(directory, matrix.file, genes.file, barcodes.file, make.feat.unique)

Arguments

directory	Absolute pathway to directory containing the three files
matrix.file	Specify .mtx file name. Default = matrix.mtx
genes.file	Specify file name for genes. Default = genes.tsv
barcodes.file	Specify file name for barcodes. Default = barcodes.tsv
make.feat.unique	Should non-unique gene names be made unique.
verbose	Logical Should function messages be printed?

Value

Sparse matrix of counts

Examples

Read10X_output(directory = 'path/to/folder/', matrix.file = 'matrix.mtx', genes.file = 'genes.tsv', barcodes.file = 'barcodes.tsv', make.feat.unique = TRUE)

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.